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Full-Text Articles in Physical Sciences and Mathematics
Using Cuda To Enhance Data Processing Of Variant Call Format Files For Statistical Genetic Analysis, Heather Mckinnon
Using Cuda To Enhance Data Processing Of Variant Call Format Files For Statistical Genetic Analysis, Heather Mckinnon
All Graduate Projects
Utilizing the power of GPU parallel processing with CUDA can speed up the processing of Variant Call Format (VCF) files and statistical analysis of genomic data. A software package designed toward this purpose would be beneficial to genetic researchers by saving them time which they could spend on other aspects of their research. A data set containing genetics from a study of trichome production in Mimulus guttatus, or yellow monkey flower, was used to develop a package to test the effectiveness of GPU parallel processing versus serial executions. After a serial version of the code was generated and benchmarked, OpenACC …
High Performance Computing Techniques To Better Understand Protein Conformational Space, Arpita Joshi
High Performance Computing Techniques To Better Understand Protein Conformational Space, Arpita Joshi
Graduate Doctoral Dissertations
This thesis presents an amalgamation of high performance computing techniques to get better insight into protein molecular dynamics. Key aspects of protein function and dynamics can be learned from their conformational space. Datasets that represent the complex nuances of a protein molecule are high dimensional. Efficient dimensionality reduction becomes indispensable for the analysis of such exorbitant datasets. Dimensionality reduction forms a formidable portion of this work and its application has been explored for other datasets as well. It begins with the parallelization of a known non-liner feature reduction algorithm called Isomap. The code for the algorithm was re-written in C …
A Dynamic Run-Profile Energy-Aware Approach For Scheduling Computationally Intensive Bioinformatics Applications, Sachin Pawaskar, Hesham Ali
A Dynamic Run-Profile Energy-Aware Approach For Scheduling Computationally Intensive Bioinformatics Applications, Sachin Pawaskar, Hesham Ali
Computer Science Faculty Proceedings & Presentations
High Performance Computing (HPC) resources are housed in large datacenters, which consume exorbitant amounts of energy and are quickly demanding attention from businesses as they result in high operating costs. On the other hand HPC environments have been very useful to researchers in many emerging areas in life sciences such as Bioinformatics and Medical Informatics. In an earlier work, we introduced a dynamic model for energy aware scheduling (EAS) in a HPC environment; the model is domain agnostic and incorporates both the deadline parameter as well as energy parameters for computationally intensive applications. Our proposed EAS model incorporates 2-phases. In …
Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz
Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz
Theses and Dissertations
Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of two …
On The Tradeoff Between Speedup And Energy Consumption In High Performance Computing – A Bioinformatics Case Study, Sachin Pawaskar, Hesham Ali
On The Tradeoff Between Speedup And Energy Consumption In High Performance Computing – A Bioinformatics Case Study, Sachin Pawaskar, Hesham Ali
Computer Science Faculty Proceedings & Presentations
High Performance Computing has been very useful to researchers in the Bioinformatics, Medical and related fields. The bioinformatics domain is rich in applications that require extracting useful information from very large and continuously growing sequence of databases. Automated techniques such as DNA sequencers, DNA microarrays & others are continually growing the dataset that is stored in large public databases such as GenBank and Protein DataBank. Most methods used for analyzing genetic/protein data have been found to be extremely computationally intensive, providing motivation for the use of powerful computers or systems with high throughput characteristics. In this paper, we provide a …